The End of the Millennium
by I.C. Weener
Summary: Some people seemed to think my previous BotW story was a little boring. This is my response.
1. Chapter 1

" _If Mipha did figure out a way to have a kid with Link, do you think it would be a very peaceful and modest situation where she tends to the egg/baby/whatever in the privacy of her ocean palace, or would the world remain at war with the Yiga after Calamity Ganon's defeat and it would be like a Conan the Barbarian thing where she's wounded in battle while she's still pregnant and Link has to give her an emergency C-section in the middle of the battlefield so she can see their child with her own eyes before dying a glorious Champion's death?"_

\- Some random post on GameFAQs that has nothing to do with this fanfic

* * *

Link was surrounded in bloody chaos. Metal clashed around him as the spears of Zoras and the swords of Hylian knights met the feral blades of Yiga tribesmen. Calamity Ganon had been thrown back into the abyss nearly a year ago, yet the struggle never completely ended. Hyrule had saved itself from instant annihilation only slowly fall into ruin each day since.

After their plot to empower Ganon with the corrupted Divine Beasts and Guardians had barely been halted by the Champions, the Yiga only became more desperate and vicious toward the rest of the realm. Now they aimed to revive the Calamity using pieces of an ancient witch doctor's mask, an artifact so powerful it was said it could cause great disasters, lay curses on entire countries, and even control the orbit of the moon. The mask had been shattered into pieces and buried far away in the four corners of Hyrule eons ago, with one fragment hidden deep in Zora's Domain. Where the Yiga had been quiet and secretive before, now they were savage and ruthless, swarming like wasps that had been shaken out of their hive.

The Yiga were charging straight for the palace stairs. Link, the Hylian knights, and the Zora marines were outnumbered and nearly exhausted. Just as a Yiga knife was about to descend into his back, the Zora Champion shielded him with her trident and impaled the assassin on her prongs.

Mipha struck at the Yiga horde with all of Vah Ruta's vengeance. Twirling her staff and screaming, she slashed through the attackers in waves of destruction. Link raised the Master Sword and fought at his wife's side.

The cowardly killing blow came from behind.

A lone Yiga in a cloak and a pig's mask rose up while Mipha was distracted, plunging a spear through the back of her kidney. The Lightscale Trident dropped out of her claws and clattered to the marble walkway. Mipha staggered forward in agony clutching the side of her belly. Her heavy, child-filled belly.

The pig Yiga cackled like a high-pitched hyena. Mipha's gold eyes sparked in rage as she snapped around and lifted her wrist. Quills flew out of the extended fin on her forearm and struck the murderer in his throat. He dropped to the ground foaming through his mask, dying from a fatal dose of Zora venom.

Mipha's eyes fluttered as she stumbled backwards. Link dropped the Hylian Shield and the Master Sword so he could catch his wife before she fell. She landed draped across his knees.

Tears formed in the corners of her eyes as she grimaced. Her hand stayed firmly over her stomach as she struggled to breathe. The ferryman was starting to take her.

"Link…" she gasped in pain, "I'm too weak… my powers… I can't save us both…"

Link tried to comfort her as she shivered through her breaths, feeling herself sink deeper and deeper into darkness. All hope seemed lost, until the Master Sword flickered dim blue on the ground beside them.

A soft chime resonated in its steel to draw their attention. It was singing to them, sending a sign to both of them. Mipha knew what it was trying to say.

"The sword," she said as she winced. "She was made to protect life. It's the only way."

Link hesitated. The fear of bringing even more harm to his wife and his unborn child made him doubt all of his skill. Mipha gazed into his eyes and guided his hand over her waist.

"Please, let me see our child before I depart for the Silent Shores."

Link regained his focus. He lifted the Master Sword an inch off the ground and brought the edge to Mipha's scales. The blade continued to glow as it moved with a will seemingly of its own. Its aura kept Link's trembling fingers steady and guided his arm, showing him where to carefully carve so he could rescue their precious treasure. Calamity Ganon had schemed for ages to hack through Mipha's flesh in his mindless path of slaughter, and he nearly succeeded a year ago. Now Link was forced to do the same thing with his own hands, for a much different reason.

Mipha clenched her teeth and wailed through her fangs. She drew on what little magic she could to dull the pain and keep herself still.

An infant's cry serenaded over the sounds of war and death. A tiny jewel covered in thin ruby silt shimmered in the crook of Link's arm. She was a beautiful baby girl with red hair like her mother and webbed gold fins over her ears like her father. Her features were predominantly Hylian, with tiny gills tucked into her neck and bright yellow Zora eyes lighting up her round pink face.

Link nestled the wailing baby under her mother's chin. Mipha smiled through her torment, spending her last moments stroking her daughter lovingly on her head.

"Take care of her, Link," Mipha said to her husband in a trickle of a whisper. "Keep my Pearl safe."

The princess sighed a final time and proudly joined her ancestors.

Link bowed over his wife for only a moment, stifling his grief for a later hour. The battle still raged around him and it was all the time he had. He leaned down to give Mipha a kiss goodnight on her forehead.

Gently, he unclasped the brilliant blue Champion robe from her left shoulder. He swaddled Pearl in her mother's mantle before rising back to his feet.

Link charged back into the Yiga horde, rejoining the other Hylians and Zoras in their fight for survival. He cut through the fray with the Master Sword in one hand and his infant daughter in the other.

* * *

 _Author's note: This is the new timeline. I hope you like it. The old timeline is the one where Mipha just sort of stands there while Waterblight Ganon decapitates her and her arc with Link has no payoff.  
_


	2. Chapter 2

" _Take good care of my daughter."_

\- Chidori 1, Ayashi no Ceres: Episode of Miku

" _Somebody get me the Ghostbusters."_

\- Mayor Lenny, Ghostbusters II

* * *

The moon was rising in an ominous purple haze. The Yiga were on the verge of completing their terrible ritual. Link was by himself in the basement aqueducts of the cult's shrine, collapsed against stone masonry with a red pool growing around him, cast down as a broken hero.

Torches crackled across the wall behind him. The sound of gently tricking water ran under his feet. Pounding war drums and tribal dancing echoed from the distant floor above.

The water sloshed in the darkness below. A sleek shadow rose out of the black ripples and climbed on to the dry cement where Link had been defeated. She loomed toward the helpless old knight like a shark closing on her prey.

The shade reached her pale pink hand over Link's heart. Just when it seemed like she was going to clench her fingers and rip the dwindling life out of him, she began restoring him with a healing aura.

Exhausted from his beating and delirious from blood loss, Link could only make out a few of her features. A long red blur dangled from the sides of her head. Her eyes were like two beams of sunlight shining through the ocean surface.

"Mi…pha…" he said in a weak and shallow breath. "I'm ready… to go with you…"

He grit his teeth as sensation returned to his mending ribs. A fraction of his strength returned, clearing his vision. The foggy visage of the deceased Zora Champion turned into the worried face of her daughter.

Pearl was wearing a common Hylian dress with a low collar that kept her gills uncovered. Vah Ruta's mantle was tied around her waist, adding an extra layer to her Hylian skirt and creating the appearance of light blue fins flaring from the sides of her legs. It had been 17 years since her mother gave up her life so her daughter could live on.

Pearl had followed her father's trail into the shrine, determined to help him even if she wasn't sure how. Her natural affinity for swimming had allowed her to slip under the Yiga patrols and breach the shrine completely undetected. After all, they were expecting their enemy to be a land dweller.

She very gently pulled away the polished Zora Shield pinning down his left arm. Her fingers crept under his right arm and carefully retrieved the Master Sword with its scabbard.

"Pearl… you can't…" Link struggled to warn her, barely keeping his eyes open, each breath creating more agony for his lungs. "I promised you wouldn't get hurt…"

The torches above them suddenly flickered. The flames mysteriously changed from bright red to dim green. The air flowing through the aqueducts turned musty and thick, like the inside of an ancient tomb. An eerie chill crawled up both of their backs.

They had never felt more at peace.

Pearl remembered the frightening times when she was a child, when her father was busy fighting off another Yiga attack, when Uncle Daruk wasn't there to let her ride on his shoulders and Auntie Urbosa couldn't tell her a story about a fearless warrior slaying a giant desert monster. When she was truly scared and she was completely alone, her invisible friend Mimi would always come to keep her company. Pearl couldn't remember how young she had been the last time she felt that strange but comforting presence brushing her head and singing her a lullaby as gentle as rippling water, but now the same feeling came rushing back.

At the same time, Link heard the green flames whisper through their crackles. A silent voice told him he had done more than any father possibly could. He had protected Pearl when she was small and helpless. He had helped her grow strong and now she could protect herself.

"Thanks, Mipha…" Link uttered in a weak sigh. His head lowered as he drifted to sleep. The flames returned to normal as the air grew warm again.

Pearl moved her palm away from her father's wounds. Her powers had rescued him from the brink of death, but his body still needed time to recover on its own.

She'd have to come back for him once the Yiga had been dealt with. If another patrol happened to find him now, his breathing was so weak that they'd easily mistake him for dead and leave him to rot. Death was the safest place for him right now.

"Rest easy, papa. I won't let everything you taught me go to waste," Pearl whispered to his peacefully sleeping form.

She stood up armed with her father's sword and shield and tied in her mother's robe. The distant stomping over her head grew louder and more urgent. She followed the stone vaults until they lead to a spillway, making her way upstream toward the Yiga ceremony.

* * *

 _Author's note: And so ends this weird gender flipped version of Wolf Children._

 _Author's note 2: I was going to put a more in-depth thing here but I ended up posting it on my blog. You can read the whole breakdown at abicion dot tumblr dot com post/171264025712/_


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